[2024-01-24 13:01:53,331] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:53,334] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:53,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg980dde1e-594c-4f5e-85ba-163332dbd85b/dqc_reference
[2024-01-24 13:01:54,627] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:54,628] [INFO] Task started: Prodigal
[2024-01-24 13:01:54,628] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f27c974-1896-41c2-a333-30be179eb14f/GCF_007989485.1_ASM798948v1_genomic.fna.gz | prodigal -d GCF_007989485.1_ASM798948v1_genomic.fna/cds.fna -a GCF_007989485.1_ASM798948v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:09,329] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:09,330] [INFO] Task started: HMMsearch
[2024-01-24 13:02:09,330] [INFO] Running command: hmmsearch --tblout GCF_007989485.1_ASM798948v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg980dde1e-594c-4f5e-85ba-163332dbd85b/dqc_reference/reference_markers.hmm GCF_007989485.1_ASM798948v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:09,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:09,703] [INFO] Found 6/6 markers.
[2024-01-24 13:02:09,761] [INFO] Query marker FASTA was written to GCF_007989485.1_ASM798948v1_genomic.fna/markers.fasta
[2024-01-24 13:02:09,761] [INFO] Task started: Blastn
[2024-01-24 13:02:09,761] [INFO] Running command: blastn -query GCF_007989485.1_ASM798948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg980dde1e-594c-4f5e-85ba-163332dbd85b/dqc_reference/reference_markers.fasta -out GCF_007989485.1_ASM798948v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:10,915] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:10,919] [INFO] Selected 13 target genomes.
[2024-01-24 13:02:10,919] [INFO] Target genome list was writen to GCF_007989485.1_ASM798948v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:10,922] [INFO] Task started: fastANI
[2024-01-24 13:02:10,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f27c974-1896-41c2-a333-30be179eb14f/GCF_007989485.1_ASM798948v1_genomic.fna.gz --refList GCF_007989485.1_ASM798948v1_genomic.fna/target_genomes.txt --output GCF_007989485.1_ASM798948v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:24,930] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:24,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg980dde1e-594c-4f5e-85ba-163332dbd85b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:24,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg980dde1e-594c-4f5e-85ba-163332dbd85b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:24,942] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:24,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:24,943] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	100.0	1613	1619	95	conclusive
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	99.9984	1615	1619	95	conclusive
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	91.4132	1092	1619	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	91.411	1090	1619	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	91.1346	1164	1619	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	91.0279	1144	1619	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	89.1254	972	1619	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	88.9391	928	1619	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	84.3123	783	1619	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.2469	698	1619	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.2413	563	1619	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.6343	627	1619	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.8833	520	1619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:24,945] [INFO] DFAST Taxonomy check result was written to GCF_007989485.1_ASM798948v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:24,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:24,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:24,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg980dde1e-594c-4f5e-85ba-163332dbd85b/dqc_reference/checkm_data
[2024-01-24 13:02:24,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:25,001] [INFO] Task started: CheckM
[2024-01-24 13:02:25,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989485.1_ASM798948v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989485.1_ASM798948v1_genomic.fna/checkm_input GCF_007989485.1_ASM798948v1_genomic.fna/checkm_result
[2024-01-24 13:03:15,685] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:15,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:15,711] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:15,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:15,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989485.1_ASM798948v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:15,712] [INFO] Task started: Blastn
[2024-01-24 13:03:15,712] [INFO] Running command: blastn -query GCF_007989485.1_ASM798948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg980dde1e-594c-4f5e-85ba-163332dbd85b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989485.1_ASM798948v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:17,750] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:17,755] [INFO] Selected 7 target genomes.
[2024-01-24 13:03:17,755] [INFO] Target genome list was writen to GCF_007989485.1_ASM798948v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:17,759] [INFO] Task started: fastANI
[2024-01-24 13:03:17,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f27c974-1896-41c2-a333-30be179eb14f/GCF_007989485.1_ASM798948v1_genomic.fna.gz --refList GCF_007989485.1_ASM798948v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989485.1_ASM798948v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:26,279] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:26,292] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:26,292] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900100045.1	s__Paracoccus denitrificans	99.9984	1615	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	conclusive
GCF_001447385.1	s__Paracoccus sp001447385	92.1127	1128	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824185.1	s__Paracoccus pantotrophus	91.3993	1091	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_000763885.1	s__Paracoccus versutus	91.0338	1143	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_000518925.1	s__Paracoccus sp000518925	90.9743	1086	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_016446475.1	s__Paracoccus binzhouensis	89.118	973	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156255.1	s__Paracoccus thiocyanatus	88.9235	929	1619	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:26,294] [INFO] GTDB search result was written to GCF_007989485.1_ASM798948v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:26,294] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:26,297] [INFO] DFAST_QC result json was written to GCF_007989485.1_ASM798948v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:26,297] [INFO] DFAST_QC completed!
[2024-01-24 13:03:26,297] [INFO] Total running time: 0h1m33s